The Soul Merger
by olalo
Summary: A young boy, Jimmy, discovers his ability to merge with Pokemon and use their abilities. With such great power, enemies are easily made. Team Rocket are back in business and experimenting on Pokemon. As Jimmy learns to control his power, he must fight through the greed and jealousy to unlock the truth behind it all. Only one thing is certain, Jimmy can't trust anyone anymore.
1. Chapter 1: He Has Returned

It was a cold night in New Bark Town. The few houses in the small town were a fair distance apart. The architecture was modern, brick and wooden walls along with a smooth wooden roof. A small garden was being grown. The flowers were close together, each a different color and scent, sending a fresh aroma throughout the town.

But nobody could have predicted what happened that night.

"Coast is clear, boss."

A group of seven men dressed in full black suits, along with a black ski mask over their faces, crept into the small town. Each of them had a few PokeBalls strapped around their waste, along with a gun and some extra ammunition.

They walked up to Professor Elm's laboratory, which had some of the most advanced technology known to the Pokemon world. The group's boss, who could be identified by his unique badge on his clothing, ducked and pulled out two clips to pick the lock.

The boss took out a small machine with a wire and connected it to the lab's security system, which hacked the security code and turned off the security. "Security is down. Stay quiet and find the three rare Pokemon. Once we have those, mission is over."

The lab was filled with light coming from the machines, but the main light on the ceiling was turned off. In the corner of the room was a small healing machine, with 6 PokeBall slots. Four shelves with glass windows stood. Inside sat different documents and accessories.

One of the men found a machine that looked like no other machine in the lab. "Boss, I found something," he whispered.

His boss and the rest of the team walked over to him. The machine had a big, red light on top of it. On the front of it was a hand recognition system to open what was inside it.

"Don't touch the machine. I'm going to get Professor Elm's hand," the boss said. "All of you stay here." The boss pulled out his pistol and attached a silencer to it. He walked out of the lab without closing the door to minimize the amount of noise he made and walked up the stairs to the Professor's house. He picked the lock and quietly entered the house.

The kitchen was to his left as he walked in, with a basic fridge, stove, and sink along with a blue counter surrounding them. To his right was the living room, with a large TV, two couches, a table, and a bookshelf.

He continued down the hall of the house and pointed his gun to the door of the bedroom. He slowly turned the knob and sneaked inside the room.

The professor and his wife slept in the bed, side-by-side. Her head was snuggled under his arm like a baby. _I hate this kind of work._ He pointed the pistol at Elm's head and shot. Despite the suppressor the sound of a firing gun woke up his wife, so he shot her too.

He pulled out a knife from his waist belt and cut the professor's arm off. Without wasting any time, he walked out of the room. As he walked by Elm's son's room, he noticed it was slightly open. _I could have sworn that the room was closed._ He stopped thinking and headed back to the laboratory.

Elm's son peered through the slightly opened door as his family's murderer exited his house. He rushed to his parents' room and saw their bodies, motionless. The bed was soaked with blood, shocking the boy into unconsciousness.

The boss returned to the lab and put the hand on the hand recognition system. The machine opened, revealing three PokeBalls. "Good work, team," the boss complimented. Chuckling darkly, he put the three PokeBalls on his waist belt and fled the town with his team.

* * *

Jimmy awoke to the screams of several town residents at six in the morning. He sprang out of bed without changing into any regular clothing.

His room was clean, not like most people his age. The TV was on the edge of his room covered in dust, along with his Wii game system. His laptop sat on his table which he did most of his schoolwork on.

He had a black T-shirt on and gold-colored shorts. His blue eyes were as clear as the sky, but his unusual hairstyle sometimes went over his face, covering his eyes. His hair was a natural black with a tuft that stuck out.

He grabbed his hat and ran down the stairs, but his mom wasn't there. "Looks like she woke up too," he said to himself. The fridge was wide open, so Jimmy jumped over his counter and grabbed an apple and took a bite. With the apple in his right hand, he ran outside to see what all the commotion was about.

Several officers parked their motorcycles and cars in front of the professor's lab and home. An ambulance was also parked, but much closer to the entrance of the house. Two men put a body-bag in the back of the ambulance and a few seconds later, two other men came down the stairs with a new body-bag.

"Jimmy!" his mom cried out. She ran up to him and hugged him. "You won't believe what happened," she said and wiped tears off her face.

"What happened here?" Jimmy asked.

She breathed in and stopped crying. "Professor Elm and his wife were murdered during the night. His son," she paused, her eyes growing watery again. "After their son woke up from being unconscious, he called the police which arrived here in a few minutes."

Jimmy's eyes widened. "But…but Elm was like a father to me."

"I know it's hard. His and his wife's funeral will be in the route past Cherrygrove. They'll be buried next to Mr. Pokemon's house."

"I'm guessing school is canceled?" Jimmy joked, even though it was uncalled for.

"Stay strong, champ," his mom said and patted him on the back.

Jimmy threw his apple on the ground, splattering into different pieces. He couldn't control the anger that raged inside of him. Because it was too early to see any real Pokemon battles to relieve his anger and stress, he decided to find a different way to see a battle.

He took out his PokeGear and dialed someone's number. "Hey Neo, it's me Jimmy. I'm coming down for a few."

"Hey no problem. It's Tyrogue vs. a Hitmonlee down here. Money on who?"

"Twenty bucks on the Tyrogue. Those things are fighters," Jimmy joked.

Jimmy made his way to Cherrygrove City, which had a Pokemon Center and Mart. It's where most new trainers stopped to get some items before leaving on their Pokemon journey. Jimmy had always dreamed of becoming a trainer and venturing the world, but he lacked the skills and the money.

He walked into one of the old, worn out houses and went down the stairs to the basement.

Many people crowded around a big ring, with two Pokemon inside it. One was a beat-up Tyrogue from earlier in the battle and the other was a Hitmonlee without a scratch on it.

"Hey, Jimmy!" Neo said. He had long, red hair and wore a black and red jacket with white pants. "Your Tyrogue isn't holding up. Hand over the twenty."

All the pent up anger inside him soon turned to pity as he saw the bedraggled and bloody Tyrogue in the corner of the ring. "Wait a second," Jimmy said. "Look at how beat up Tyrogue is. You're supposed to take them out of the ring at this stage."

"It's not up to me, Jimmy. The people want a fight."

"Not if I have anything to say," Jimmy said and jumped into the ring. "Come on, Tyrogue. I'm taking you to a Pokemon Center." He grabbed the Tyrogue and ran out of the ring.

"Hey, where do you think you're going?" said one of the thugs. "I put my money on that little guy!"

Jimmy sprinted up the stairs and headed to the Pokemon Center. He looked back to see if he had been followed, but it seems like they didn't care enough. "Please, heal this Pokemon. He's all beat up."

"Don't worry, with these new machines we can heal Pokemon instantly, even if they were in the worst condition," she said and took the Tyrogue. She put him in a PokeBall and placed him on a machine on the counter. The PokeBall glowed for a few seconds and then stopped. The Nurse took the PokeBall off the machine and released the Tyrogue. "Good as new in seconds!"

"You all right, little Tyrogue?" Jimmy asked. He had never met the Pokemon in his life, but he felt a connection between them. "Good as new." He chuckled and looked down at the Tyrogue.

The Tyrogue jumped on Jimmy, hugged him, and began to shine brightly. When the brightness stopped, the Tyrogue was gone.

"What in the world?"

The thug and a few of his thug friends bashed through the doors of the Pokemon Center. "Hey man, I believe you've got something we want."

"Looks guys, the Tyrogue literally just disappeared," Jimmy responded. "I have no idea where he went."

"Then I guess you're going to take the beating he was supposed to get." The thug walked up to Jimmy and cracked his knuckles. "Are you ready?"

_Come on Tyrogue!_

The thug threw a punch at him, but Jimmy moved his head and pushed the thug's hand to the side. Jimmy side-kicked him in the face and the thug fell back onto some plants.

"I guess I underestimated you," the thug said as he got back up. He wiped the blood off his lip and charged at Jimmy, but Jimmy moved to the side right as he was about to get hit and pushed the thug forward with a kick, stopping his momentum and smacking him into the counter.

_What just happened?_

The rest of the thugs ran out of the Pokemon Center, afraid of getting the same beating as their friend.

"Good work, trainer!" the Nurse exclaimed. "More people should be as brave as you. I'm calling the police right now!"

Jimmy sat down on one of the seats, still unclear of what happened. _Where'd you go, Tyrogue? And how did I beat up that thug?_

A male officer entered the Pokemon Center and arrested the thug. "May I ask what happened here?"

"Well, the thug came in talking about some Pokemon that I saved from a beating," Jimmy stopped before continuing. _He'll think I'm crazy if I tell him the Pokemon disappeared…_ "And so he tried to fight for it back and attacked me, but I fought back and defeated him. By the time I looked to see where the Tyrogue was, well, it was gone."

"Can I see the surveillance footage please? It just seems a little farfetched, no offence."

"None taken."

The Nurse led the officer to the surveillance room and he saw that the Tyrogue disappeared after a bright flash of light. "He has returned."

The officer ran back to the main room of the Pokemon Center and dialed a number on his PokeGear. "Sir, tell the Johto Security Agency that he has returned!"

Jimmy overheard the conversation, but didn't pay much attention. He was deep in thought. The memories of the Tyrogue played in his head, as if he was there. As if he was the Tyrogue.

A JSA agent dressed in black walked into the Pokemon Center. "What are you talking about? This is not him!"

"Look at the footage! If it's not him, then it's another one!" the officer said, leading the agent into the surveillance room where he saw the bright flash.

"I can't believe it. After three years, we've found another one to complete the mission!" the agent exclaimed.

"Come with me, Jimmy," the agent said. "We have a lot to talk about."

The agent escorted Jimmy to the car. Jimmy had seen a JSA agent who had saved several people before, so he trusted the JSA. He believed it had something to do with what happened earlier, so he got in the car.

"We're going to take you to a high-level government facility. Trust me, everything will be explained," the agent said.

* * *

The agent opened the door for Jimmy and led him to the house that they had parked next to. It was a small house in Ecruteak City and was in the style of all the houses in that city: wooden walls, wooden roof, wooden everything.

One man was in the room, sitting on the floor and meditating. "Did you bring the boy with you, Agent Oak?" he asked, but his voice was weak.

"Yes Grandpa, he's here," the agent responded. "Sorry for how mysterious things happened earlier. My name is Agent Gary Oak, member of the Johto and Kanto Security Agency, but currently I'm stationed in Johto."

"And who is he?" Jimmy asked.

"That's my Grandpa. You probably know him as Professor Oak."

"No way! THE Professor Oak?!" Jimmy asked. He was a big fan of him ever since Professor Elm told him the great stories when Elm was under Oak's teaching.

"Yes, it's me. But I need you to be serious now," Professor Oak said and stood up. "The ability you possess is powerful and I see that you have merged with your first Pokemon already."

"Merged? You mean…me and that Tyrogue…we're the same person?!" Jimmy exclaimed.

"Actually, that Tyrogue is now part of your memory. Everything the Tyrogue was and what it can do is locked in your memory."

"Is that how I was able to beat up the thug?"

"Precisely. You triggered Tyrogue's skills by thinking of Tyrogue. You had a surge of energy and were able to use his skills. But this surge of energy is only temporary and it cannot be used constantly, or else you might kill yourself in the process."

"So, could I merge with other Pokemon if I wanted to?"

"It's not that simple," Gary interjected. "You saved the Tyrogue, which created a special bond between the two of you. This special bond allowed you to merge with it and a bond is always needed for a merge."

"Are you guys just here to explain it to me? Or is there a greater purpose to this meeting?" Jimmy asked impatiently.

"You Soul Mergers are all the same," Oak chuckled. "The reason you are here is because your services are needed. You are going to become a JSA agent and work on a secret operation built on defeating Team Rocket."

"Is Team Rocket by any chance connected to the murder of Professor Elm?" Jimmy asked.

"Yes, the footage showed that trained Rocket agents did this, but fortunately not trained enough," Gary said. "One of them wasn't wearing gloves and we got a fingerprint, which identified one of their agents."

"So did you guys interrogate him or what? I'm not familiar with the drill."

"We haven't captured him yet. And that's where you come in," Oak said. "He's here in Ecruteak City. We took you to this JSA base for a reason. I'd honestly prefer taking you to my hometown in Kanto to brief you, but our Rocket agent and his friends are in the Burnt Tower as we speak. And your first mission awaits."

"So let me get this straight: I have the ability to merge with Pokemon, use superhuman skills, and am an official member of the JSA?"

"That's correct," Oak said.

"Great, let's get to my first mission."

* * *

**Hey guys, thanks for reading! Any suggestions, comments, criticism, etc. is much appreciated! You can point out any grammatical or spelling errors you may find and I will fix them as soon as I can. If you have questions or concerns about the story, you can feel free to say them although I do have the entire story more or less planned and I have written up to Chapter 5 although each chapter is constantly being reviewed. Just want to see what people think about the first chapter before uploading more to see if there's any changes that need to be made. Admittedly the story is very fast paced, but it's all for good reason. What seems to be a light-hearted adventure story will soon turn dark and suspenseful. Keep going with it and I promise you will not be disappointed. My writing may not be the best, but I make up for that in plot. Once again, thanks and don't be afraid to comment!**


	2. Chapter 2: Traitor

**Chapter Two: Traitor**

Jimmy looked up at the Burnt Tower. It was the largest building in the Johto region, but nobody was ever brave enough to climb to the top of it.

Many myths are told about the tower's history; how there was a disastrous fire and the legendary Pokemon saved it from being destroyed.

The stairs leading towards the Burnt Tower had been made with new wood, but the tower itself was named a historical landmark. Nobody was allowed polish it in any way to keep the history for centuries to come.

He walked up the stairs to the tower. The door creaked open as he entered the room.

There were countless holes on the floor that when looked into only led to darkness. The sounds of wild Zubats and Koffings echoed throughout the first floor, but none approached Jimmy.

"Hey Gary, I'm in," Jimmy whispered into his PokeGear.

"They wouldn't be stupid enough to discuss their plans on the first floor," Gary said. "They probably went downstairs. It's said that ghosts live there, so nobody would go there and spy on them."

"I'm turning my PokeGear off. Don't want to make unneeded noise," Jimmy said and pressed a red button on his PokeGear.

He put it back on his waist belt and searched the room. The first level was where tourists went to see the fire's effect on the tower and the Pokemon living there.

At the edge of the first level was a hole, with a ladder sticking out of it. "Looks like I found my way down." He approached the hole and looked through it before going down. It was too dark to see anything, but a crying sound echoed through the underground level.

Jimmy silently went down the ladder and took out his flashlight. He set it on the lowest brightness level to attract the least amount of attention.

He followed down a narrow hallway, but could barely see anything. The crying got louder as he walked and the hallway became brighter, as if another light source was being used at the end of it.

Jimmy turned a corner and noticed three Rocket grunts and two dark figures. Through the shadows Jimmy couldn't identify them clearly, but he could see they weren't wearing Rocket uniforms.

"It seems like the Legendary Pokemon are deeper underground than we had first calculated," a Rocket grunt said.

"First you said they were going to be on the first floor, then the underground level, now you want us to go deeper?" a shadowy figure exclaimed loudly.

"Please Morty, we can't go back with failure. Giovanni will scold us," the other shadow figure responded.

_Morty? The Gym Leader?_

"Alright Eusine, tell the Geodude to dig deeper," Morty said. "I'll contact the other Gym Leaders in Team Rocket."

Jimmy's PokeGear got loose from his waist belt and fell on the floor, creating a loud 'dink' sound. "Crud."

"Hey, who's there?" a Rocket grunt asked and walked towards the corner. The Rocket grunt looked around, but couldn't see anyone.

Jimmy jumped from around the corner and punched the grunt in the face. The grunt nearly tripped on himself, but regained his balance.

"You have no idea who you're messing with, kid," the grunt said and pulled out his pistol. "What are you doing here?"

"Take care of the kid and the Legendary Beasts, Eusine. This isn't my problem anymore," Morty said. He walked past Jimmy and exited the underground level.

"Nobody is here to save you, so why don't you tell us why you're here?" Eusine asked.

"Well, here goes nothing," Jimmy said. _Let's do this, Tyrogue_. A surge of energy pulsed through his brain, playing memories of Tyrogue training in Cherrygrove City against wild Pokemon.

Jimmy grabbed the grunt's hand and twisted it, forcing him to drop the gun. He kicked the grunt in the chest and pushed him into another grunt. "Who's next?"

The last grunt tried to reach for his gun, but Jimmy jabbed him in the face and side-kicked him in the chest, pushing him against the wall.

"I'm always up for a good fight," Eusine chuckled. He cracked his knuckles and got into a fighting stance, one fist up and the other on the side of his hip.

Eusine jabbed with his front fist, but Jimmy blocked it and kneed him in the chest. While Eusine was regaining his balance, Jimmy reached for the gun that the grunt had dropped and pointed it at Eusine. "I wouldn't suggest you make another move." Jimmy picked up his PokeGear that he had dropped and called Gary. "I've got the bad guys. One escaped, but I identified him. We should be able to get him too."

In seconds, Gary and a trained team of agents entered the underground level.

"Eusine, so good to see you again," Gary said as he hand-cuffed him.

"Your new agent here is good," Eusine said with a small chuckle of defeat.

Jimmy crouched down and looked at the Geodude. "You can stop digging," Jimmy said, hoping the Pokemon would understand.

The Rock Pokemon stopped digging and climbed back up the hole he had dug. He smiled and opened up one of his fists.

"A high five?" Jimmy asked. He slapped his hand down on Geodude, and with a bright flash, Geodude was gone. "I don't understand. I just saved him. Doesn't he want to be free with the other Pokemon in the world?"

"We'll talk about this later, not with Rocket grunts in the room," Gary said.

* * *

Gary locked the prisoners in the underground prison of the Ecruteak JSA base and rejoined with Jimmy on the first floor.

"Mind giving me an explanation now?" Jimmy asked, growing impatient.

"Like I told you before, the Pokemon is repaying you by giving you his powers. The Geodude is still alive, but inside of you. The more you use the powers he gave you, the more powerful Geodude will become inside of you."

"I sort of get it," Jimmy said. "What are we going to do about Morty? He left before I fought the Rocket grunts and he also mentioned something about other Gym Leaders being involved in Team Rocket."

"Already ahead of you," Gary smirked. "One of the professor's stolen Pokemon was being held by the Rocket grunt. It's a Cyndaquil." He pressed the middle button on the PokeBall and a red beam of light transformed into the fire Pokemon. A small flame sat on its back. When the flame was small, the Pokemon was calm and collected, but when the flame grew, it meant it was angry or battle-ready.

"Wow? Does it have any clues or something?" Jimmy asked.

"No," Gary chuckled, amused by Jimmy's lack of understanding. "You're going to challenge Morty to a 1-on-1 Gym Battle."

"But I hardly know the Pokemon!"

"Then here's your chance to befriend it. Every agent needs a partner Pokemon. Mine is Blastoise. Yours will be Cyndaquil. Try not to merge with it," Gary joked and patted Jimmy on the back. "You better get going before Morty realizes his team was captured." Gary threw Jimmy the PokeBall for the Cyndaquil. "Take good care of him."

Jimmy pointed the PokeBall at the Cyndaquil and put him back in it. "Come on, little buddy."

* * *

Jimmy walked through the doors to the gym, but it was almost pitch-black. "Light the way," Jimmy said and let the Cyndaquil out of his PokeBall.

The Cyndaquil's flame grew on his back, nearly lighting up the whole room.

Morty looked up to see his challenger, but his hopeful expression turned into an angered one. His blonde hair reached down to his shoulders and his blue headband was wrapped tightly around his head. "Are you here to arrest me?"

"I'm here to battle you, Morty. How about I make you a deal?" Jimmy asked. "I beat you in a Pokemon battle and you tell me who the other Rocket Gym Leaders are. You'll also be arrested."

"What's in it for me if I beat you?"

"You'll walk. We won't arrest you or question you. Take my word for it." The Cyndaquil walked up in front of Jimmy and the flame on its back grew even larger.

"Quite a big flame you're racking up there," Morty said. "Think it can take on my Haunter?" He threw his PokeBall into the air and released his ghostly Pokemon.

The Haunter's dark face was lit up by the flame's light. His tongue was sticking out, almost like it was laughing at its opponent. Its two claw arms floated next to his body, but weren't connected to it.

"Scared yet?" Morty smirked. "Haunter, use Lick!" Morty commanded.

Without Jimmy's command, the Cyndaquil jumped over the Haunter as it rushed at him and shot a series of flames out of his mouth.

"Now I see why Rocket wanted this Cyndaquil so bad," Jimmy said.

Smoke filled the room as the flames collided with the ghost Pokemon, but the Haunter shook it off.

"Haunter, use Shadow Ball!" The Haunter's arms came closer together and a dark blob formed in between his hands. The Haunter released the shadow attack at the Cyndaquil, but the Cyndaquil retaliated with his own Flamethrower attack.

The two attacks collided, but did not explode. The Cyndaquil's Flamethrower seemed to be pushing the Shadow Ball back to the Haunter, but the Shadow Ball also became stronger and pushed the Flamethrower back.

The power struggle ended as the Cyndaquil released all of his remaining strength into the attack. The Shadow Ball flew back at the Haunter, followed by the powerful Flamethrower attack. The collision between the Haunter and the powerful attacks caused a massive explosion.

Smoke covered the battlefield, causing both trainers to cough. As it slowly settled, the Cyndaquil's flame became visible. The Haunter was on the ground, defeated and knocked out.

"You're under arrest, Morty."

"No, it can't end like this!" Morty screamed. He pulled out a pistol and aimed it at Jimmy. "Give me one good reason not to pull the trigger!"

_Geodude!_

A surge pulsed through his brain, similar to that of Tyrogue. Images and memories of Geodude throwing rocks at wild Pokemon played through his head.

"I can't give you a reason," Jimmy said.

Morty pulled the trigger and the bullet rushed towards Jimmy. In that split second, Jimmy raised a wall of stone from the ground and blocked the bullet. He moved his hands forward and the wall of stone rushed towards Morty and smacked into him. He flew backwards and hit the wall at the back of the gym.

Jimmy ran up to Morty and grabbed him by his collar. "Who are the other Gym Leaders?"

Morty tried to headbutt Jimmy, but Jimmy's skin was as hard as rock. Blood trickled down Morty's forehead and into his mouth. He spit it out on Jimmy's face and smiled. "You really think I'll tell you anything?"

Jimmy jabbed Morty in the face, knocking him out. He pulled out his PokeGear and called Gary. "Bag and tag him."

* * *

"Good work, Jimmy," Gary said. "You're officially a member of this operation, which means that you get your very own alias."

"You mean like in the movies?" Jimmy joked.

"You need to take this seriously. You are now called Agent Gold. We don't want Team Rocket to find out our agents' real names. I already made that mistake before," Gary explained. "And from now on, you will call me Agent Blue. Understood?"

Jimmy nodded his head. "What do we do about Morty? We need to interrogate him. Get the information he knows. Who knows what Team Rocket could be up to next?"

"Don't worry about that, leave that to us. Right now, what you need is a good night's rest."

Before leaving the room, Jimmy took one last look at the Cyndaquil's PokeBall.

"Professor Elm would have wanted you to have that Cyndaquil," Gary said.

"I just can't believe he's gone. He taught me everything I know. How to tie my shoes, how to properly eat, and even how to cook scrambled eggs," Jimmy said. "He was truly like a father to me…"

"Don't trouble yourself with these thoughts. We'll find who did this to the professor, I promise," Professor Oak said as he walked into the Ecruteak JSA base. "I heard the way that man talked about you. He believed you had so much potential and he was right. He just didn't know what kind of potential you possessed."

"Grandpa is right. We'll find him," Gary said. "And when we do, that person will be locked up forever."

"Thanks guys," Jimmy said. "What's our plan for tomorrow? What's our next move?"

"We don't have the plan yet. A new agent will be joining our team tomorrow and will help us come up with something. I know you're still new to the way things work, but try not to break under the pressure so quickly." Gary patted Jimmy on the back and went to his room.

Professor Oak followed Gary to his quarters. "This whole operation rests on that boy's shoulders," Oak said. "Train him well. He'll need it for what's to come."

* * *

"Boss, our team was captured, along with Morty and Elm's Pokemon," a Rocket grunt spoke into a phone.

"Do we know who is responsible for this?"

"It's Agent Blue and his team. What do you want me to do?"

"Giovanni wants Blue alive and that's what he's going to get," the boss chuckled darkly. "He won't even know what's coming."

* * *

Jimmy walked into his room. In the corner was a bed with a nightstand right beside it. The rest of the room was entirely empty. _I'm in way over my head_, he thought. He lay down on the bed and closed his eyes, hoping to get some rest.

The sound of three knocks came from the door. "Come in."

Oak slowly stepped into the room and stood by the bed. His face showed a look of concern. "Jimmy," he began. "I know this is all moving very fast. We have contacted your mother and told her you are assisting us in some routine work. What I want you to know is that we are doing everything in our power to keep you out of harm's way. The level of danger the mission today reached was unexpected."

Jimmy smiled. _It's nice to be appreciated for once_, he thought. "Don't worry, Professor. I am here voluntarily and I will do everything in my power to stop Team Rocket from harming anyone else. When they killed Professor Elm, they made this personal."

"Good, good. Use the anger. Let me drive you forward. But don't let yourself become lost in it. The path of revenge is a difficult one to return from."

"Is that what happened to the other one like me?" Jimmy questioned and looked up at Oak.

"Now that is a story for another time. Get some rest now, child. You'll need it for the days to come."

* * *

**And that's the end of Chapter 2! Any comments/questions/suggestions/criticism etc. are much appreciated. It's a light-hearted start to a pretty dark story so enjoy the happiness while it lasts. Hope you all liked it!**


	3. Chapter 3: Inner Darkness

**Chapter Three: Inner Darkness**

A Rocket grunt entered a small room. It was full of books stacked on shelves. There was a small desk in the center, along with a man seated behind it.

"This better be good news," the man said. "I don't need you wasting my time."

The grunt was shaking. He was nervous to be standing in front of his boss. "Boss, sir, everything is going according to plan. The Rocket grunts that were captured yesterday activated their tracking devices, which we placed inside of them so JSA wouldn't notice," he said.

"And where is their location?" the Boss replied.

"In Ecruteak City, sir, in a small building next to the Pokemon center," he said. "Should I send a team there?"

"Wait until my order, I will tell you when to strike." He got up and took a book off his shelf. It was called 'The Secrets of Dragon Pokemon'. "In the meantime, get the team ready. We're sending in our best men."

* * *

Jimmy yawned loudly as he got out of bed. Through his window, he could see the sun was out, but it was a bit cloudy. He got dressed and placed his PokeBall on his waist belt. He went into the main room and poured himself some coffee.

He enjoyed the architecture of Ecruteak city. It had an old feeling to it. Almost every house was made of fine wood, except for a few exceptions.

He sat down and took out his PokeGear. There was a text message from his mother which read: "Have a great day. Love you!"

Gary came up from behind him and patted him on the back. "How'd you sleep?"

"Fine," Jimmy replied. "What are today's plans?"

Just as he said this, a woman entered the base. She wore a tight, red shirt with a white jacket over it. Her black and yellow shorts were very short, not hitting anywhere near her knees. She had two pigtails, but they weren't normal. They went down to her shoulders, and then slanted upwards, almost like Jimmy's tuft. Her hair was crystal-colored, but most of it was covered by a cap on her head.

"Good morning, boys," she said. "Let's get down to business, shall we?" Her voice was intelligent. She did not stutter or hesitate. Neither of the boys responded. They were shocked by how she looked. "Snap out of it boys!" she said and smacked the table with her fist. "My name is Agent Crystal and I have been assigned to your team. So please, let's get to business."

Gary shook his head. "Sure, what did you have in mind?" he asked.

"Morty has intel we need. Good thing for me, I know just how to extract information out of men," she said as she repositioned her bra, pushing up her boobs. She pulled out a small knife from her pocket and made her way towards the holding cells.

* * *

Morty was tied to a chair with his hands behind his back. His head slouched down, but as soon as Crystal entered the room, he looked up. He smiled creepily and licked his lips. "Is this the kind of people they send to interrogate criminals these days? Young bimbos?"

Crystal pulled her arm back and sent it back at Morty. A backhand slap to the face left Morty with a bright red mark on his cheek. "Please, keep talking. Give me more reasons to hurt you." Her face revealed no emotion. She stared blankly at Morty, who was still shocked by the slap.

"Oh the things I would do to you if my hands weren't tied," he said with a smile. He slowly brought his face up and stared right back at Crystal. "Those big, beautiful bo-," but before he could finish, Crystal pulled out her knife and stabbed him in the upper leg. "AHH, you whore!" Blood oozed out of the wound and down his leg.

"Tell me what other Gym Leaders are compromised and I'll let you keep your leg," she said as she drew the knife closer to him.

"You're going to have to try harder than that," Morty said and spat in her face.

"Tell me who they are!" She repeatedly stabbed Morty all around the first wound. Morty screamed out in pain. "Next thing I stab into is your crotch. Give me a reason not to or you will no longer be considered a man," she said as she wiped the blood off her knife on Morty's pants.

Morty remained silent. "Alright, your decision." She inched the knife closer and closer to his crotch until the tip of the knife pressed up against his pants. "One last chance. Tell me what I want and you get to keep it," she said, pointing at his crotch. Sweat dripped down Morty's forehead. His teeth shook as the tip of the knife cut through the pants and pushed up against his skin.

Crystal pushed the tip of the knife through Morty's skin. He screamed out in pain.

"Okay! Stop! I'll tell you everything you need to know. Just please, stop!"

* * *

Crystal walked out of the holding cell and back to Gary and Jimmy. "The two other compromised Gym Leaders are Chuck and Claire. I've already contacted headquarters. They've ordered Agent Gold and I to get Chuck. Agent Blue, you have been ordered to stay here."

"What, why?" Jimmy questioned. "I think we'll need as many agents as possible for a mission like this."  
"It's an order from the top. It's not a negotiation." Her response was quick, cold, and cruel. She did not care for how Jimmy might feel about this decision, at all. "Agents take orders. You're an agent now."

"Don't worry about it, Jimmy. I'll be fine here at the base. I'll keep gramps some company." He got up and went to his room.

"So, how do you plan on doing this?" Jimmy asked. "What's the game plan?"

She opened up a map of the Johto region. "Our private jet will drop us off at Olivine City. Landing straight in Cianwood City will alarm Rocket operatives. Instead, we will take a ship all the way to Cianwood from the Olivine Port. Got it?"

"Got it."

* * *

The jet landed near the Battle Tower. It was a small airfield that brought in many challengers from all across the world to fight in the Battle Tower.

Jimmy and Crystal entered the port and bought a ticket. They looked around the room. There were many different people of all shapes and sizes, but one caught Crystal's eyes. He was a tall, well-built man. She would have to keep an eye on him, just to be safe.

They entered the ship and entered their assigned rooms. "It's not going to take long," she assured Jimmy. "It's only about a half hour away."

"Gotcha." Jimmy went to his room and lay down on the bed. He tried to get some shut eye. He dozed off quickly.

His room door opened and a shadowy figure entered the room. The figure placed his palm on Jimmy's face for a moment. Then, the figure walked away and left.

Jimmy began to shake violently in the bed. Images of fire and death plagued his dreams, turning them to nightmares. One final image of the entire Johto region aflame woke him from his slumber. Sweat covered his entire body. He immediately rushed to the bathroom to clean off.

* * *

Back in Ecruteak City, Gary was looking over some surveillance footage from the night of Professor Elm's death. It was nearly impossible to identify the killers. They were caught on tape, but it was too dark out. All that could be identified was a big red 'R' plastered on their shirts. They were all wearing masks and gloves, to cover their faces and to avoid leaving fingerprints.

"I'm going to find all of you," he thought to himself. Suddenly, a loud pop noise came from the main room. Gary ran to the main room, only to find the front entrance completely blown up. Six Rocket soldiers entered the room.

They all held M4 Assault Rifles and wore tactical vests, filled with different equipment. "You're coming with us, Gary," they said and grabbed him. They handcuffed him, put a bag over his head and took him away.

Professor Oak ran to see what happened, but by the time he got to the main room, Gary was gone. He took out his PokeGear and dialed a number. "Tell Lance our base was infiltrated. If they know where we are, that means they know about Agent Gold and Crystal. Contact them immediately!"

* * *

The ship arrived at Cianwood and no call had been made. Crystal and Jimmy exited the ship.

They both looked around until they noticed the Cianwood Gym. "That's probably where Chuck is hiding. We will surprise attack him using the back entrance of the gym," Crystal said.

Jimmy followed behind her as they approached the gym. They entered the gym from the back and were amazed. There was a waterfall in the center and several staircases on the sides. Many black belts were training with each other. The ones without partners were using punching bags to train. Several even trained with their Pokemon.

Chuck was completely unaware of his surroundings. He was under the waterfall, meditating.

"Does anybody know how to turn off the waterfall?" Crystal shouted. None of the fighters listened, except one, who made his way down to her from the upper level.

"Chuck usually makes us fight you before you fight him, but because you're a girl, I'll let it slide," he said in a condescending tone. "We wouldn't want to beat up on a girl."

"Turn off the waterfall before I smash your face in," she said assertively. She pushed him to the side and stood in front of Chuck. The water stopped running and Chuck opened his eyes.

"Well, well, well. Looks like we have ourselves some challengers, huh?" His muscles were huge. His tone was tough. His pants were ripped and his black belt was tied tightly around his waist. "One on one? Two on two? What's your battle style?" he asked.

Before Crystal could answer, Claire interrupted. She jumped down from one of the higher levels and landed next to Chuck. "Chuck, these people are JSA. We need to take them out," she said. "Come on girl, I can take you," she said confidently.

Crystal went for a cross-punch, but Claire blocked it with one hand and proceeded to roundhouse kick Crystal in the chest. The strike landed and Crystal fell backwards; the wind knocked out of her.

She slowly got back up, but her feet shook. She was struggling to regain her strength.

Jimmy came forward and confronted Chuck. "Come on Chuck, think you can take me on?"

_Geodude!_

A surge pulsed through his brain. Images of Geodude blocking attacks from Pokemon played through his head.

"Confident, aren't you? I like that!" Chuck replied. Jimmy went for a punch to the face, but Chuck grabbed his fist. "Strong grip, I can feel it. But it's not going to be enough."

Chuck twisted Jimmy's arm and kicked him in the chest, sending him flying backwards.

"How did you do that? I'm made of freaking rocks!" Jimmy shouted.

"Don't you know, young man? Fighting is strong against Rock," Chuck said. "JSA scum. Not even trained properly!"

"I'm trained perfectly well!" _Come on, Tyrogue_! Images of Tyrogue punching rocks played through his head. "I may not be as strong as Rock now, but at least I can fight properly," Jimmy thought.

Chuck tried kicking Jimmy again, but he dodged the kick and countered with his own kick. Chuck stumbled backwards, but quickly regained his balance. "I've had enough of this kid!" He crouched down and started sprinting towards Jimmy. He slammed his head into Jimmy's chest, sending the boy flying backwards again. This time, Jimmy's head smashed into the wall behind him and he blacked out.

"Good work, Chuck," Claire said as she pulled out a tranquilizing gun. She pointed it at Crystal and shot a dart. Crystal fell on the ground, unconscious. She walked over to Jimmy's body and checked his pulse. There was nothing. "You killed the boy! He could have told us useful information." She shook her head. "Never mind this. Take the girl to the chopper. I'll be waiting for you."

Chuck picked up Crystal's body and disappeared with Claire.

* * *

Jimmy opened his eyes and took a deep, loud gasp. He was in a small room, lying on a bed. There was a needle right next to him, but it was empty. He took a look around and saw a man with orange hair. "Wow, I never thought it would work on a human, but I guess it does!" the man said.

"What? What is going on?"

"Ssh, lie down. Let me explain everything," he said. "After all the commotion going on in the gym, some of the local policemen went to check what happened. What they found was, well, you! They checked your pulse, but there was none. So they brought you here, to me. I am a doctor, but mostly a Pokemon doctor. I checked your pulse again, and I found one. It was extremely faint, but it was there. I injected a full serum of my famous Secret Potion, and here you are, alive!"

It took a few seconds for Jimmy to digest what he had just heard. "What about a girl? Did they find a girl? My age? Weird hairdo?"

"No, the police only found you. I'm sorry, was there someone else with you?" he asked. "By the way, the police will probably want to know what happened."

Jimmy jumped out of bed, but he could feel the pain in his chest from where he was hit. He took out his PokeGear and dialed Gary's number, but there was no answer. Instead, he dialed Professor Oak's number.

"Hello? Jimmy is that you?" Oak asked. "Where are you?"

"I'm at Cianwood. They kidnapped Crystal. I'm alive, but injured," he replied.

"I'm sending a chopper your way. It'll wait for you in the outskirts of Cianwood."

* * *

A Rocket grunt took the bag off of Gary's head. He was sitting in a pitch-black room and tied to a chair.

A spotlight shined on a man, but his identity was still unclear. "Welcome to Rocket Headquarters, Gary," he said in a deep voice.

Gary struggled in the chair, trying to free himself, but it was of no use. "What do you want from me?"

The man laughed. "Gary, you've got it all wrong. The real question is, what do you want from us? Ever since the first Soul Merger, we've noticed your behavioral change. Jealousy and anger consumed you. If you help us Gary, we can help you too."

Gary's eyes lit up. "I…I don't understand. Tell me who you are!"

Another Rocket grunt entered the room. He was holding a needle. It had some weird liquid in it, along with a tiny device that would also enter his bloodstream. He injected Gary with the serum and left the room.

"What we just did there was put in your body a device that could explode anytime we wanted it to," the man said. "You either help us, or you die. There's really no other choice."

"I'd…I'd rather die!" Gary shouted and spat on the ground. "You're a bunch of crooks."

The room's lights turned on. Gary looked around and saw another room to his left that was separated by a window. In the room, Crystal was tied up just like Gary. A Rocket grunt had a gun pointed to her head.

"Don't you touch her!" he shouted. "Don't you lay a finger on her!"

"It's up to you, Gary. You bring us your new agent, the Soul Merger, and we give you the powers you've always wanted. And of course, we'll give you your little girlfriend back." He walked up closer to Gary. "Do we have a deal?"

Gary could finally identify the man. "Yes we do, Giovanni."

"Good, we're going to release you now. What you're going to do is lead a fake operation at one of my operative's base. All the coordinates and information will be sent to you on your PokeGear." He took out a knife and cut off the rope that tied up his hand. "Good luck, Gary. You are now a Rocket agent."

* * *

The chopper that picked up Jimmy from Cianwood landed in Goldenrod City. Professor Oak greeted Jimmy and led him to the new JSA base.

"Why Goldenrod? What happened to our base in Ecruteak?" Jimmy asked.

"Sit down, Jimmy," Oak said. Jimmy did what he was told. "Gary was kidnapped by Rocket from the JSA base. His location is unknown and right now, this is the only safe place you've got."

Jimmy was shocked, but his shock was soon replaced by relief, as Gary came through the front door. "Gramps, I'm…exhausted," he said as he collapsed.

"Jimmy, pick him up and get him to the bed." Jimmy picked Gary up and moved him to his room. "He must have escaped from them and sprinted all the way to this base. Let him rest. We'll talk to him in the morning."

* * *

Back in Rocket Headquarters, Giovanni was having a meeting with his recon team. "Where was the last place Agent Red was seen?"

"A few months back, our recon team spotted him in Victory Road, heading towards Mt. Silver it seemed," one of the Rocket agents said. "Sadly, they couldn't keep up with him and soon lost him."

"Anything recent?"

"In fact, there is something very recent!" Giovanni was not amused by the agent's enthusiasm. "There have been drastic weather changes in the peak of Mt. Silver. We think someone might be up there; however, nobody has ever reached the top and survived. The trip is extremely tough and the Pokemon there are even tougher. We would need someone close to the skill level of Agent Red himself."

"That is being worked on," Giovanni replied. "Good work. Train your men to withstand the cold conditions of the peak. What about a possible aircraft that could fly up to those heights and still be functional?"

The Rocket agent wrote the idea down. "We'll get our engineers working on it as soon as possible."

"We'll speak soon, men," Giovanni said and opened the door for his men to exit. He went back to his desk and began to pet his Persian. "Soon, the whole world will be crumbling at my feet. And nobody will stop me."

* * *

**End of Chapter 3! Lots of little teases all over this chapter and set up for many fun things to come! As usual, any comments/suggestions/criticism are highly appreciated. To the one reviewer I've already got, thanks for the support! I'm glad you liked it! **


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